<!-- Feel free to add brief descriptions to your research interests as well -->

<!-- Feel free to add brief descriptions to your research interests as well -->

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*Every week, month, quarter and year, I will summarize my current interest, direction, what I have done and the next plans in the following page: [[User:Pakpoom Subsoontorn/Notebook/general reading/2008/11/09 | Strategic Summary]]

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<!--*Every week, month, quarter and year, I will summarize my current interest, direction, what I have done and the next plans in the following page: [[User:Pakpoom Subsoontorn/Notebook/general reading/2008/11/09 | Strategic Summary]]-->

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==Current Research Projects==

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==Past Research Projects==

<!-- Feel free to add brief descriptions to your research interests as well -->

<!-- Feel free to add brief descriptions to your research interests as well -->

** From winter 2004 to summer 2006, I worked as an undergraduate researcher at Winfree's lab on developing new functional modules for ''in vitro'' transcirptional networks. ''In vitro'' transcriptional switches were originally developed by Jongmin Kim, a former graduate student in Winfree lab, as a stripped-down version of genetic switches in the cell. A switch consists of only DNA template, RNA polymerase and RNase. Signals are carried by the concentrations of specific RNA transcripts. RNA transcript from one switch can be used to regulate the production of RNA transcript from another switch. Thus, while a switch is biochemically simple, one could build up a complex regulatory network from collections of switches. The original version of ''in vitro'' transcriptional switches can only be negatively regulated by RNA transcript. My contribution was to design and characterize a new version of switches which can be positively regulated. I have shown that a simple bistable circuit can be implemented using a single transcriptional switch positively regulated its own RNA transcription. The switch was also later used by Jongmin to construct the first ''in vitro'' transcriptional oscillator. We are now preparing the manuscripts for publication.

** From winter 2007 to spring 2008, I worked as an undergraduate researcher at Phillips lab on the analysis of transcriptional regulation at single cell level. The goal was to provide experimental validation of statistical mechanic models for bacterial transcriptional regulation. In winter and spring 2007, I designed and tested microfluidic device for high throughput single cell microscope imaging. In summer 2007, I developed a new plug-in for image-based autofocus using [http://www.micro-manager.org/| <math>\mu</math>Manager] software as part to the tool for automated microscopy. From summer 2007 to spring 2008, as part of my senior thesis, I constructed and tested synthetic gene circuits that allow the calibration for the absolute concentration of transcription factor in a single bacterial cell (based on a system developed by Rosenfeld et. al. 2005). The system relies on the fact that variance of the transcription factor molecules segregated to daughter cells during cell division depends on the the absolute number of the transcription factors in the mother cell. In parallel, I also worked in collaboration with [http://www.vision.caltech.edu/| prof. Pietro Perona] on developing software from automated analysis of fluorescence microscopy images to be used for my data analysis. This project is still an on-going research at Phillips lab after I left Caltech.

**In fall 2008, as a rotation student, I helped prof. KC Huang set up a new at Stanford. I started pilot projects related to biophysics of bacterial cell shape. The projects include 1) using light microscope and quantitative image analysis to study how ''E.coli'' cells convert between rod shape and nearly spherical shape during the transition between exponential growth phase and stationery phase, 2) studying the mechanics of ''E.coli'' cell wall cracking induced by antibiotic vancomysin, 3) designing a microfluidic device for culturing and imaging the lineage of rod-shape bacteria.

**In winter 2009, as a rotation student, I worked on project to develop a new techniques for determining protein structure by measuring intramolecular distances using FRET. The idea is to label different pairs of amino acid residues on a protein with fluorescent donor an acceptor, measure FRET efficiency and infer the distances between each pair. The measured distances will be used as constraints to reconstruct the shape of the protein.

** Starting in spring 2009, I started a new project in Endy's lab on how to reliably store multiple bits of information in a living cell using genetically encoded devices. I designed and computationally analyzed the performance of genetically encoded combinatorial counters as a study case for high-order genetically encoded information storage systems. Our counters can take an input from arbitrary genetically encoded system and transition from one state to the next state depending on the number of input pulses it receives. Unlike earlier work in genetically encoded counters which can count up to only N states using N bits and which are sensitive to input pulse width, our counter designs could count up to 2^N-1 states and are predicted to operated robustly with respect to input pulse width. In addition, our counter architecture is highly modular at three functional levels: set-reset latches, toggle flip-flops and counters. A set-reset latch can be implemented from DNA Inversion controlled by bacteriosphage integrases-excisionase, two mutually inhibiting repressors, or single positively autoregulating activator. A toggle flip-flop can be implemented from two set-reset latches or a single set-reset latch and a relay unit with switching delay. A counter can be implemented as an asynchronous counter or a synchronous counter. Different designs at each level can readily be composed together into the next level devices, resulting in at least 12 possible ways to build counters. The performances for different choices of device implementations and kinetic parameters ranges are compared. I am now preparing the manuscript to publish. In addition, I am also working closely with Jerome Bonnet, a postdoctoral fellow in Endy's lab, on implementing DNA inversion-based set-reset latches in E.coli. We have demonstrated that the latches can be set, reset and hold state. We are now working on improving the reliability of the latch operation and possible ways to scale up the number of latches that can be engineered into a cell.

Research interests

Past Research Projects

From winter 2004 to summer 2006, I worked as an undergraduate researcher at Winfree's lab on developing new functional modules for in vitro transcirptional networks. In vitro transcriptional switches were originally developed by Jongmin Kim, a former graduate student in Winfree lab, as a stripped-down version of genetic switches in the cell. A switch consists of only DNA template, RNA polymerase and RNase. Signals are carried by the concentrations of specific RNA transcripts. RNA transcript from one switch can be used to regulate the production of RNA transcript from another switch. Thus, while a switch is biochemically simple, one could build up a complex regulatory network from collections of switches. The original version of in vitro transcriptional switches can only be negatively regulated by RNA transcript. My contribution was to design and characterize a new version of switches which can be positively regulated. I have shown that a simple bistable circuit can be implemented using a single transcriptional switch positively regulated its own RNA transcription. The switch was also later used by Jongmin to construct the first in vitro transcriptional oscillator. We are now preparing the manuscripts for publication.

From winter 2007 to spring 2008, I worked as an undergraduate researcher at Phillips lab on the analysis of transcriptional regulation at single cell level. The goal was to provide experimental validation of statistical mechanic models for bacterial transcriptional regulation. In winter and spring 2007, I designed and tested microfluidic device for high throughput single cell microscope imaging. In summer 2007, I developed a new plug-in for image-based autofocus using μManager software as part to the tool for automated microscopy. From summer 2007 to spring 2008, as part of my senior thesis, I constructed and tested synthetic gene circuits that allow the calibration for the absolute concentration of transcription factor in a single bacterial cell (based on a system developed by Rosenfeld et. al. 2005). The system relies on the fact that variance of the transcription factor molecules segregated to daughter cells during cell division depends on the the absolute number of the transcription factors in the mother cell. In parallel, I also worked in collaboration with prof. Pietro Perona on developing software from automated analysis of fluorescence microscopy images to be used for my data analysis. This project is still an on-going research at Phillips lab after I left Caltech.

In fall 2008, as a rotation student, I helped prof. KC Huang set up a new at Stanford. I started pilot projects related to biophysics of bacterial cell shape. The projects include 1) using light microscope and quantitative image analysis to study how E.coli cells convert between rod shape and nearly spherical shape during the transition between exponential growth phase and stationery phase, 2) studying the mechanics of E.coli cell wall cracking induced by antibiotic vancomysin, 3) designing a microfluidic device for culturing and imaging the lineage of rod-shape bacteria.

In winter 2009, as a rotation student, I worked on project to develop a new techniques for determining protein structure by measuring intramolecular distances using FRET. The idea is to label different pairs of amino acid residues on a protein with fluorescent donor an acceptor, measure FRET efficiency and infer the distances between each pair. The measured distances will be used as constraints to reconstruct the shape of the protein.

Current Research Projects

Starting in spring 2009, I started a new project in Endy's lab on how to reliably store multiple bits of information in a living cell using genetically encoded devices. I designed and computationally analyzed the performance of genetically encoded combinatorial counters as a study case for high-order genetically encoded information storage systems. Our counters can take an input from arbitrary genetically encoded system and transition from one state to the next state depending on the number of input pulses it receives. Unlike earlier work in genetically encoded counters which can count up to only N states using N bits and which are sensitive to input pulse width, our counter designs could count up to 2^N-1 states and are predicted to operated robustly with respect to input pulse width. In addition, our counter architecture is highly modular at three functional levels: set-reset latches, toggle flip-flops and counters. A set-reset latch can be implemented from DNA Inversion controlled by bacteriosphage integrases-excisionase, two mutually inhibiting repressors, or single positively autoregulating activator. A toggle flip-flop can be implemented from two set-reset latches or a single set-reset latch and a relay unit with switching delay. A counter can be implemented as an asynchronous counter or a synchronous counter. Different designs at each level can readily be composed together into the next level devices, resulting in at least 12 possible ways to build counters. The performances for different choices of device implementations and kinetic parameters ranges are compared. I am now preparing the manuscript to publish. In addition, I am also working closely with Jerome Bonnet, a postdoctoral fellow in Endy's lab, on implementing DNA inversion-based set-reset latches in E.coli. We have demonstrated that the latches can be set, reset and hold state. We are now working on improving the reliability of the latch operation and possible ways to scale up the number of latches that can be engineered into a cell.